Microbiome Series – Conference Highlights

Paul McAdam, one of our Bioinformatics Team Leaders, attended the Microbiome and Probiotics Series: Europe in Rotterdam in May.  With three full days packed with talks and panel discussions, we caught up with him to hear his highlights from the conference and talks.

Day One

With three streams to the conference – Microbiome Research & Development, Probiotics, and Skin Microbiome & Cosmeceuticals – Day 1 was the busiest, with speakers in all streams giving talks on a wide variety of topics.

The first keynote speaker for the Microbiome R&D stream was Karen Nelson, President of the J. Craig Venter Institute. ‘Translation of the Microbiome: are we there yet’ detailed the challenges and opportunities offered by microbiome research. There was discussion of the pros and cons of 16S vs shotgun methodologies, highlighting the trade-offs between the amount of data generated and the associated costs and analysis time. Nelson also looked at future directions for microbiome research, including research into metatranscriptomics and host-microbe interactions. She spoke about the need for more global studies, looking into different human populations to capture the broad diversity present across the globe.

The second keynote was given by Dirk Hadrich, Policy and Programme Officer at the European Commission for Health Research, Personalised Medicine, DG Research & Innovation. With almost half a billion Euros invested to date by the EU in collaborative microbiome research, Hadrich highlighted the success those projects. The MetaHIT project was one of the first microbiome studies funded by the EU. It produced a catalogue of gut microbes and enterotypes (a classification scheme for the gut microbiome). MetaHIT aimed to find associations between bacterial genes with human health and disease. Two other projects highlighted were MetaCardis, a study of the role of gut microbes in cardiometabolic diseases, and SYSCID, a systems medicine approach to chronic inflammatory diseases. 2019 sees the start of three new EU-funded projects researching the role of the microbiome in disease focussing on cancer, liver failure, and autism.  Of particular interest, the cancer study aims to produce a cancer microbiome ‘atlas’, through recruitment of 9,000 patients, producing a comprehensive resource for future research.

Dr Adam Baker, Head of Discovery – Microbiome and Human Health at Chr. Hansen, spoke next on innovations in probiotics. The microbiome is a source of probiotics and live bacterial therapeutics, many of which have a beneficial effect on human health. Baker presented research from a recently published study that demonstrated that a strain of Bifidobacterium breve has a protective effect against damage caused by long-term aspirin treatment, assessed through use of capsule endoscopy.  This finding offers a therapeutic benefit for people taking long-term cardioprotective aspirin treatment.

Arne Materna, Vice President of Product at CosmosID, spoke about the importance of standardisation and reproducibility in for metagenomic studies in order to effectively compare results from different studies.  He highlighted that in many cases where microbial diversity and host contamination are low, shallow depths of shotgun sequencing can be appropriate, yielding high-resolution data at a comparable price to 16S sequencing.

Dr. Nikole Kimes, founder and CSO of Siolta Therapeutics, presented research highlighting the role of the gut microbiome on the development of chronic inflammatory conditions such as asthma and allergy. Siolta have promising pre-clinical data demonstrating the use of live microbial therapeutics to promote immune tolerance, treat the symptoms of asthma, and prevent asthma before it develops.

The final talk of day 1 was given by Dr Morten Isaksen, CEO of Bio-Me. Bio-Me’s Precision Microbiome Profiling (PMP) platform is a qPCR-based assay targeting up to 200 of the most common commensal bacteria at the species and strain level.  In contrast to 16S and shotgun sequencing methods, the PMP platforms promises same day profiling of microbiome samples at a high resolution. This rapid turnaround time is a great benefit to researchers and clinicians working and can accelerate decision making.

Day Two

Day 2 kicked off with Dr Marie Drago, founder of Gallinée, talking about the scalp microbiome. Gallinée are a cosmeceutical company producing probiotic products to support the skin microbiome. Their products aim to improve skin and scalp health by maintaining a pH that allows the natural microbiome to thrive and play a protective role. Drago discussed the known association of Staphylococcus epidermidis with dandruff, and the potential to treat dandruff through modulating the microbiome.

Hansoo Park, CSO of Genome & Company, spoke on the human microbiome and cancer. Studies have shown that the gut microbiome can affect a patient’s response to cancer immunotherapy. Genome & Company are leveraging data from multi-multi-omics studies to identify single strains of bacteria that have a synergistic effects with anti-PD1 therapies.  It is hoped that further development can lead to anti-cancer therapeutics derived from the microbiome that have a real benefit to patients.

One of the key themes that came up throughout the conference was the role of the microbiome on chronic inflammatory diseases. Myeong Soo Park of BIFIDO presented data showing enrichment of Prevotella species in patients with new-onset rheumatoid arthritis (RA).  Conversely, the relative abundance of Bifidobacterium spp. was reduced.  BIFIDO found that treatment with a specific strain of Bifidobacterium reduced arthritis score comparable to on-market therapies in mouse models, possibly through modulation of IgG2a.

Research coming from TargEDys focussed on modulating the appetite through the microbiome. Grégory Lambert, CEO and Vice President of R&D, spoke of their new supplement called ProbioSatys.  ProbioSatys aims to regulate appetite through molecules that mimic of α-MSH, a hormone that promotes a feeling of fullness.  A bacterial analogue, ClpB is a mimetic of α-MSH, and can promote a feeling of satiety, leading to a reduction in food intake in mouse models.

The final talk from the second day was by Bloom Science’s CSO, Christopher Reyes. Reyes’ talk focussed on the gut-brain axis, and the effect of microbiome in neurological disorders.  The ketogenic diet has been shown to be an effective intervention for children with drug-resistant epilepsy and the effect has been shown to be in part due to changes in the gut microbiome. Reyes presented data showing that an increase in the relative abundance of Akkermensia spp. is sufficient to reduce seizure burden, and offers an intriguing avenue of research for future therapeutics.

Day Three

Day 3 rounded off with talks on gut microbiota-host interactions and personalised precision medicine.

Adrien Nivoliez, CEO at Biose opened the day with a talk highlighting the challenges of scaling up production of live biotherapeutics. As a contract developer and manufacturer, Biose provide a GMP-certified manufacturing facility to guarantee quality and consistency for companies looking to take their product to market.

Next up, Sandra Robelet, CSO of Syncrosome, showed the range of preclinical models available from the company.  With established models for conditions where the microbiome has been implicated, such as diabetes, inflammatory bowel disease, and asthma among others, the company can provide relevant experimental conditions for drug testing of novel biotherapeutics.

COO of ARTPred, Jonathan de Jonge, spoke about a successful collaboration between industry and clinicians resulting in the development of a microbiome-based test to predict success of IVF treatment. ARTPred is focussed on improving fertility treatment, and has focussed on the urogenital microbiome and improving IVF success rates.  Together with clinicians, ARTPred have developed a predictive test for IVF outcomes, ReceptIVFity. The test profiles the vaginal microbiome to give an indication of the likely success of IVF treatment.

The final talk for the day – and the conference – was given by Momo Vuyisich, CSO of Viome. Viome have developed algorithms for ‘precision nutrition’ to design personalised diets for their customers. Using data collected, Viome have been able to take an integrated approach, using -omics, nutrition, and clinical data from customers to build predictive models for several chronic inflammatory conditions. Viome have also been able to give a ‘personalised glycaemic response’ through their algorithms which can predict glycaemic response to foods approaching 80% accuracy.

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